Cable vibration hum was always a pretty good indicator for us back in the day. That, and bubbles coming off what appears to be the top 12" of cable. FWIW my GPS speed is usually just under a full mph higher than my ball speed.
Doubt it was a Sturgeon. I've done that twice and both times they were very lazy. Probably knowing they could do anything they want at any time. Probably a fouled King, but a Musky is a possibility or a big cat.
When you are getting to that size range 28' and above, the stability of a straight inboard and ease of maintenance wins out.
I/O"s aren't even in the conversation.
Same situation for me while Island camping in the St. Lawrence. Tow Boat told me 3-4 hrs. I drifted to shore and tied up to a tree, next to a private launch. The owner allowed me the time to walk 3 mi to my truck and come back and use his launch. I did all this in under 3 hrs. Never renewed with TowBoat.
Not sure what you mean by locations near Rochester. I think it gets you perks at West Marine but the Roch store is pretty useless IMO. Better off investing in a reliable kicker!
You can switch the Perko from 1 to 2 or to both, while running without issue. The problem is if you accidently switch to off while doing so. That could be a real bad day!
Is the control wireless? I have heard the wireless Trollmaster's do the same thing. If it's not wireless, try isolating the wires from other electrical harnesses. Maybe run it through some flex conduit?